Kristin's World

A diary of Kristin's musings on conservation, technology, and Just Being.

Monday, September 01, 2008

PlanetWare.Net

At long last, I am pursuing this long-held idea of starting my own software company focused on software solutions for environmental problems. I’ll start out with consulting, add staff and customers and move to independent product development as opportunities arise. And for this venture, I've secured the domain name "PlanetWare.Net"

The mission of PlanetWare.Net will be to bring the power of software technology to the problems of the environment. We build software for a healthy planet. (Of course, at the moment, “we” is refers to the “royal we.” ;) We'll combine software development expertise, experience in natural resources conservation and other environmental issues with a proven ability to deliver world-class solutions for diverse customers.

Our services include development consulting in technology strategy, system architecture, product definition, project management, software development and user experience. Overtime, the company will independently offer software products, perhaps in the area of water resources management, ecosystem services valuation (that is, systematic economic valuation of clean air, clean and plentiful water and other stuff in-tact ecosystems give us “for free”) and environmental systems data integration. Or somethin’ like that.

I've got my first contract and am building the foundation of a small business. What? Am I Scared? Nah! I'm terrified. But thanks to great friends, family, Pema Chödrön and The Buddha, it's all good.

By the way, the image to the left is an early prototype for a PlanetWare.Net logo. Let me know what you think!

0 Comments:

Thursday, May 15, 2008

The Case for Conservation Information Systems

As promised, I'm beginning a series of posts based on components of my master's research. I'll begin by answering this basic question: why should anyone care? That is, why would we in conservation who have so few dollars to address the enormous need we face spend any money or even time on information systems?

Here's my answer: The game is changing. Conservation of natural systems has moved from a personal value to a requirement for living. Our historical focus on species loss and sprawl must broaden dramatically to include issues as complex and integrated as climate change, water. The Nature Conservancy's marketing department is already on the job: "Last great places" has been replaced by "Protecting nature. Preserving life." On the information side of the house, the conservation comunity must recognize and respond to the need for a new level of scientifically rigorous, defensable information to guide, improve and account for our actions.

Environmental conservation has always had to answer the question, what and how do we conserve? After all, limited resources and compelling alternatives are nothing new. But the more sophisticated answers mean higher demands on information.

Conservation 1.0. In its early form, human conservation of natual systems has focused on the protection of beautiful, "wild" places and the species that compell us. The criteria for conservation was thus subjective, even intuitive. Who needs an information systems for that? We see it, we love it, we protect it. Simple. Protecting a place is straightforward. Protecting a species usually means protecting habitat. So we'll need good ecology and habitat maps. Not so simple, but usally doable given that clear focus.

Conservation 2.0. We've known for a while now that the sixth great extinction is underway, anthropogneic in origin. Translation: massive critter die off, our fault. The Endangered Species Act moved us beyond the "charasmatic" critieria and instead asked questions about species' rarity. Now we're studying a lot more ecology and mapping a lot more habitat in the context of government accountability for the recovery of nature's rare elements. Then E.O. Wilson coined the term “biodiversity” as we recognized the need to preserve the full bounty of nature's creatures and habitats and conservation took up the charge. With more sophisticated analyses of critical species habitat, richness, rarity or irreplacibility we identified "hot spots" that gave us big biodiversity bang for our buck. Uh oh. We might need some serious information systems to help us understand a whole slew of species habitats and their conditions. Who has this data, how do we get it, integrate it (so easy to say, so hard to do), and analyze it?

Conservation 3.0. Present day. By necessity, the conservation agenda must respond to at least five new realities, all with significant ramifications for our information systems requirements:

People really do need natureAwareness of the human dependency on functioning natural systems is on the rise and with it the need to explicitly value the services provided by intact, functioning natural systems. This view recognizes conservation’s role in informing tradeoffs in the ongoing human domestication of nature. Valuation of ecosystem services depends on highly quantitative, spatially-explicit, multi-scaled analyses based on both biophysical and socioeconomic datasets.

Global Climate ChangeSuddently, effective conservation depends on forcasting nature's response to a changing climate. Tall freckin' order! We must develop models of biodiversity response to changing conditions at a scale that can inform natural resource management and landscape planning. These analyses themselves must accomodated improvements in prediction algorithms and the granularity and accuracy of input datasets.

No more “go it alone”Both assessments and action increasingly require of conservation organizations deep collaborations with each other, partners in government and the private sector. To effect decision making, assessments across the spectrum of conservation subjects, from the condition of individual species to integrated regional land-use planning, increasingly require contributions from multiple organizations and disciplines. Similarly, implementation of conservation projects more and more often involves active participation of cooperating organizations. Effective collaboration depends on information sharing and integration.

Scale MattersConservation biology increasingly recognizes that the geographic scale at which analyses are performed changes the questions asked and answered. As a result, multi-scale assessments are required to effectively inform decision making within a given region.

Account and AdaptFinally, the business of conservation is under increased pressure from the donors and the public to account for its spending and objectively measure outcomes of its strategies. Adaptive management specifically requires that we do no “wait for science;” rather measure and respond to measurement of our actions themselves.

All of the changes above translate to growing, not shrinking, demands on effective information systems. Conservation must adapt to the changes underway in its core business. The era of intuitive valuation of conservation priorities has ended. Donors and societies must know that their investments in conservation are based on rigorous and informed analysis. We may not be particularly good at this stuff today, but we better get good at it and quick. We risk fidelity to our mission as well as relevancy to society if we do not invest in the information systems capacity required to protect nature and preserve life.

1 Comments:

Both assessments and action increasingly require of conservation organizations deep collaborations with each other, partners in government and the private sector.

I'd like to point out that social networking technology makes meaningful action by individuals possible by aggregating it. I work for a company that was founded on the idea of allowing individuals to both assess and take action on climate change (admittedly only one part of the conservation equation); see a blog post on our early attempts here: http://www.readwriteweb.com/archives/brighter_planet.php.

Friday, April 25, 2008

Blue Devil Milestone

It's been a long great ride. With my adviser's approval, I have submitted my master's project to Duke. Grateful to all of those who have supported my efforts not just during this project but this degree, I am finished and awash in relief. Only the ritual and celebration remains (okay, the some of celebrations have already started).

When I graduated from the University of Texas at Austin with my computer science degree (way back when), I couldn't give a hoot about graduation ceremonies. While challenging, the completion of that degree was never really in question. On May 11th, 2008, however, I'll be doning that blue cap and gown with pride and receive this master's diploma grinning wide. For this degree was in question many times: it was through grit and grace that this moment has arrived.

For your loyalty, I'm going to punish all of you readers (both of you?) by selecting portions of my project and posting them here. I mightily encourage your comments: ideas, suggestions, criticisms, questions or just musings. So get ready, here comes An Information Systems Strategy for the Conservation Community.

0 Comments:

Tuesday, December 04, 2007

Here's another great post I ran across on the blog "Joel on Software." I love reading this guy, Joel Spolsky, because, while I don't always agree with his points, he is consistently insightful, practical and sometimes eloquent about the strange new business of writing software. I found this particular post somewhat relevant to some (surprisingly sane) discussions we've been having at the Nature Conservancy on technology stacks/application patterns and deeply relevant to the 100 years technology war (or so it seems) all of us in the software industry been living through.

If you enjoy this, check out his recent posts recounting a talk he gave at Yale, his alma mater.

0 Comments:

Tuesday, November 20, 2007

Harvesting Data for ConservationPart 2: The Solution

In 2002, The Heinz Center released its report on ecosystem conditions in the United Stated, “The State of the Nation’s Ecosystems.” The authors declared the assessment as incomplete due to the lack of data collection, reporting and systems infrastructure to sufficiently assess ecosystem condition. Yet the reality is that between the efforts of academic researchers, local and national governments and conservation organizations, an enormous amount of information deeply relevant to conservation is being collected, even in digital form. However, variation in syntax (e.g., file format) and semantics (e.g., termonology) prevent practical aggregation and analysis of collected data.

In my last post, I described this fundamental problem in conservation information systems, that of data model variability. I described how the variation in the schema of common conservation information systems entities such as observations, protected areas, conservation projects, conservation activities frustrates our ability to provide rich data entry/management applications as well as aggregation and analysis capabilities, capabilities that would significantly inform assessments like "The State of the Nations Ecosystems."

The solution is to develop a system that supports rich data entry/management/reporting and yet is independent of a specific data model. The system would treat the definition of entities such as observations or protected areas as data itself. Each of these entities has a core schema, the set of attributes that makes it what it is. A species observation, for instance, consists of an observer (person), location, date and time, and a species identifier. This core can then be augmented with observation attributes from a library (e.g. egg count, nest height, stratum, life stage). When needed, more advanced users can build their own attributes (solarization, acidity) and submit them to the common attribute library. Finally, the entity core schema and a selected set of extended attributes can be combined into an extended entity schema. Extended entity schema are useful for repeated use potentially reflecting and enforcing a standard or protocol. The library, shared across the natural resources management community, can thus contain core and extended entity schema and their component entity attributes.

For instance, a standard field protocol for surveying invasive species can be captured in a invasive-species observation schema and applied in numerous invasive species surveys. The schema can be extended to support surveys of specific invasives. (For instance, it was determined the length of the hind legs on the invasive Cane Toad was correlated with the geographical front edge of the invasion. "Hind Leg Length" would then be a key attribute of a survey of Cane Toads.)

The data management application parses the entity schema and component attributes as the definition of data types and behaviors. It then provides rich data entry, management, mapping, reporting, spatial and statistical analysis on the entered data. We can afford to invest heavily in the development of this system because the functionality is not specific to a given conservation data model. Attribute definitions are localizable into other languages including labels, help text, error messages, a feature critical for global conservation. Thus ends the tyranny of the software engineer. No longer are users beholden to software developers to create custom applications with rich functionality to support their data models, data models can that evolve with the needs of conservation and basic scientific understanding.

The other win for conservation is the ability to aggregate and analyze the resulting datasets arising from conservation organizations, the academic research community, even state agencies. When users populate datasets based on shared entity schema and extended attribute definitions, these datasets are inherently standardized and available for rich analysis. For instance ,species observation data can be harvested and mapped across all species surveys (using secure web services) for their common core (observer, observed species, date/time, location). Even this basic map would constitute a major breakthrough for conservation. Analysis of invasive species observations, based on an invasive species observation schema, would similarly bring insights to patterns in invasions. Population reductions or migrations over time associated with climate change can be mapped and analyzed based on surveys where climate change, per se, was not the primary focus of the survey. Again, while this approach would enable conservation to make use of an enormous wealth of basic observation data, these concepts apply equally well to information about lands managed for conservation (protected areas), stewardship activities, conservation projects themselves, etc.

We developed such a simple with a small team at NatureServe to support observations. The data entry/management/reporting tool is rich in functionality and yet supports any data model we could think throw at it. Parks Canada is the first customer and is already excited about the ability to support users conducting specialized surveys within parks and as well as those carrying out high level analysis of observation data across parks.

There is nothing specific to conservation in this technology. Indeed, I see examples of related systems existing and emerging on the web. Freebase is the closest I've seen yet to supporting what we need. But I'm not sure Metaweb is going where we need to go.

For instance, the support for combinations of attribute definitions into entity schema, corresponding to basic entities in conservation like observations and protected areas, is critical to support user-driven standards and protocols. We must have the ability to search and browse a community repository for core entity schema and their associated attributes. This open-source style resource would allow schema authors to post their submissions for use by the conservation community, solicit feedback, post modifications, and report on usage. In this way, subject-matter experts in various areas of conservation and biodiversity can directly share their expertise with the community in the form of widely-used entity and attribute definitions.

By separating the data model from the data management application functionality, we can provide conservation practitioners on the ground with powerful and usable tools to capture and manage their information. This same approach, to the extent we succeed in building a rich, common library of data model components, will enable unprecedented aggregation and analysis of similar, though not identical, data sets. The efficacy and efficiency of conservation at the project level can thus be improved as well as our overall understanding of the status and dynamics of nature.

5 Comments:

I've read your past few posts on data technologies for ecology and conservation and find your analysis very insightful.

Providing flexible, collaborative data structures while maintaining some semblance of shared "semantics" is a real challenge.

In an area like conservation, the importance of sharing distributed observations is even more critical than in other domains. As an Economist, I look at this as a design question: how do you develop a collaborative repository which makes the utility of the shared repository, for any individual researcher, greater than that of a private "spreadsheet" collection method.

I work at Metaweb and think these are the important questions which will determine whether shared information systems will be able to improve our world in meaning ways.

I have been working with a small, but growing community of biologists who have been developing schemas on Freebase for taxonomy, ecological models and bioinformatics. I would welcome the opportunity to work with you on the problems you outline here and talk with you about the direction Metaweb is taking.

Utility to the data producers is indeed the critical component. To acheive our goals, we simply have to beat Excel and that includes usability, performance and powerful functionality for this problem space. The very good news is that, when focused on the specific problem domain of managing conservation datasets, we definitely can beat Excel.

If we beat Excel and systems like Excel, the conservation data producer not only wins with a more suitable system to his/her problem, the conservation data consumer (aggregator/analyzer) also wins. Standards conformance, like armies in a Trojan horse, is embedded in the data management system. The data producer is producing conforming datasets without paying any additional costs. His/her data is available for downstream usage not because he's succumb to altruistic arguments about data sharing and then taken extra time and effort to cross-walk his/her data to standards, but because sharing amounts to checking a box, literally, checking a box.

It's possible and exciting. I very much believe that, as you put it, shared information systems can improve our world in meaningful ways.

I welcome the opportunity to collaborate. I'll be emailing you shortly.

Kristin, we've already discussed these ideas in some detail and I'm totally on board. I just wanted make one comment in response to yours that there is still some cost to the data producer, in that there must still be compliance with the attribute library for the full goals to be achieved. So maybe consider it a watered down conformance to standards. In the best case scenario, everything you need is already in place because somebody else did the work. In the worst case you may have to research attributes and semantics already in the library and establish your extended schema. No argument about benefits to both producers and consumers, and still a dramatically lower cost than developing a completely new system to handle the different context.

Excellent point, Paul. You are quite right that if a required attribute is truly missing from the library (or worst of all, hard to find), the data producer either abandons the system (reverting to Excel) or pays the non-trivial cost of describing a new attribute and and template.

The hope is that costs to each individual data producer converge to zero over time only because of the contributions of data producers before him or her.

In practical terms, we know what's required here to make this work for conservation: organizations like The Nature Conservancy, NatureServe, Cornell Lab of Ornithology and others can lend their expertise and capacity to the "seeding" effort. We take our existing conservation data standards and describe them in the library, thus at least reducing the costs for data producers who follow by giving them a good head start.

First, there will always be a cost when the data producer is collecting truly novel information. For instance, if "soil acidity" was only recently measurable, the associated attribute would have to be described, potentially by the first researcher to measure it in the field.

Second, we can mitigate the costs by providing powerful and user friendly functionality for defining, even localizing, new attributes and submitting them back to the community repository.

Third, besides the "seeding" idea mentioned in my previous comment, the open source approach to the shared repository might help us as well by enlisting the power of ego. Is it hard to imagine egomaniac biologists investing themselves in the task of creating attributes and templates based on their expertise? We'll create attribute and entity template usage reports (sharing the usage counts without sharing the data) that have the effect of esteeming their authors.

Thursday, November 15, 2007

Harvesting Data for ConservationPart 1: The Problem

Biodiversity Conservation, as an "industry," has not only common interest but critical need to improve a) the productivity and assessment of conservation activities and b) downstream aggregation and analysis across conservation activities. This need has been formally expressed (see conservationcommons.org). Yet its practical realization has thus far eluded us.

As I see it, the fundamental barrier to the development of rich applications to manage conservation projects as well as aggregation and analysis tools is this: data model variability. For instance, whereas a field observation consists of a fundamental core of information (observer, observed species, date/time and location), meaningful observations almost always describe more than just this core. This is in order to support the purpose of the observation activity. For example, if we're trying to understand reproduction rates among migrating bird species, an observation record will not only document the date/time, location, observer and bird species, but also the fact that this is a nest observation and how many total eggs are in the nest, how many of those appear to be in tact. An observation management system that only allows users to capture the core attributes would be useless for almost all specific observation activities.

The same is true for tracking and managing information on protected areas, stewardship activities (e.g. prescribed burns, reforestation) and other datasets critical to conservation. While there is a common core of attributes to describe these entities in conservation, users must be able to extend beyond this core in practical application.

Because of that variability of the data model, users end up pursuing one of two approaches to capture and manage their conservation datasets. The first and most prevalent option is to employ technologies that are completely generic (e.g. spreadsheets or simple databases). These systems meet immediate needs fairly well. However, their resulting datasets are completely nonstandard and therefore unavailable for aggregation with similar datasets. In this case, the needs of the data producers may be met, but data consumers are frustrated (see Mismatched Incentives).

Where aggregation of large datasets and/or specialized functionality is required, users pursue the other option: procuring the development of custom systems. Custom systems of course are developed at considerable cost and, because they are hard-bound to a static data model, these systems are suitable only for a single application or, at best, a similar class of applications. How unfortunate that our investments in conservation data management systems must be repeated for each new dataset. We can ill-afford to enrich the functionality (e.g. usability, mapping, reporting, feeds, import/export, wizards) or performance of any given system because this investment is specific to users of only a specific dataset. It is as if each dissertation, because of its unique content, required the development of a new word processor.

1 Comments:

Hey Kristin. I couldn't agree more. We need minimum data models for the core conservation entities, including conservation projects, protected areas, and species and ecosystem occurrences. How do we get there?

Thursday, November 01, 2007

Changing Jerseys

As many of you know, I was enjoying my work at NatureServe. At the same time, starting last June, I began to see through various connections signs of positive change in The Nature Conservancy's approach to information systems development including an improved governance, deeper integration with science, accountability and software development practices. When my friend Dennis Fuze, who is in charge of all systems development there, told me he was hiring for a Director of Conservation Systems Development, it seemed like just the right role. So I jumped into the interview process (intense!) and was offered the job, reporting to same-friend Dennis.

My technology background suited the systems development folks, and the Nicholas School credentials turned out to be instrumental in swaying the conservation science and practitioners… those who will be the customers of the systems development I oversee.

So I got the job and now I’m terrified. Okay, not completely, but I am “excited.” The Conservancy is a BIG organization with all of the accompanying challenges plus a few more. It’s also one that I respect immensely, has wonderful people and unique opportunities. I am thrilled to have the chance to contribute.

I have a great team (spread all over the country!) and a challenging portfolio of existing and new projects. I'll continue to work with folks from NatureServe, now as a tough customer. I'm still in the Conservation Information Technology league, I've just switched jerseys.

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Wednesday, September 12, 2007

Mismatched Incentives

In Conservation IT, there's a lot of discussion about the "need for standards." But something about this rings authoritarian and ultimately limited.

Most aggregators and analysts of observation information agree about the imperative for data standards. They are united by their common interest in synthesis, analysis and decision support to address critical questions in natural resources management and conservation. This group recognizes both the unmet need and the missed opportunity in each observation dataset that remains in simple spreadsheet form, digitized but nonetheless disconnected. They are thus motivated to convene and deliberate, producing standards that reflect their interests in the data. They then cajole and/or coerce another group, the observation data collectors and on-the-ground researchers, to go out of their way to conform, convert, reformat, translate, crosswalk, describe and their data then upload it to shared data servers. Yet the benefits to this second group, the producers, are abstract, realized in another place and time and by someone else. Not surprisingly, observation data that is un-described, disconnected and highly variable in format and semantics continues to accumulate, the unfortunate outcome of mismatched incentives. The result is a wealth of information whose potential to inform and direct the understanding, effective management and conservation of natural systems is never realized.

Instead we need to meet the needs of information producers with great data entry, management and analysis tools that embed standards conformance, like the pollen of nieghboring flowers, in the data they produce. That is, only by meeting the needs of the data producers will we achieve standardization at the scale required by data consumers.

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Sunday, July 30, 2006

Conclusions from the Course

Cabo Blanco was mostly about wrapping up papers and having some great end-of-course parties and gave me the opportunity to think on all that I had learned over the this month experience.

I have shared with you so far much of the beauty and intrigue, large and small, of the sites we visited. But in my work and education in conservation, there was much to contemplate beyond an introduction to and appreciation of natural Costa Rica. So, along those lines, here's a smattering of impressions and ideas that struck me...

From a technology perspective, some obvious conclusions emerged. GPS: not there yet and not clear how we get there any time soon. The devices are fine, it's the canopy that's the problem. So unless you can afford an antenae to get your reading above the trees, GPS is just a nice idea. Devices in general, including field text, audio, image and video collection, are coming down in price, but under used by researches because those with sufficient durability are still prohibitively expensive. It rains a ton and if your device isn't waterproof, it's rather useless. Moreover, the degree that technology determines the scope of research projects was clarified. That is, researchers use the tools they know and answer the questions their tools can illuminate. It's easy to see how specialized technology is playing an increasingly important role in biology: gene research being the most striking example. But GIS was rarely used in our course, not because there weren't innumerable fascinating spatial questions to ask and answer with GIS, but because almost all the students lacked familiarity with the toolset. That will change as the tools improve (dramatic improvements await!), but I was struck by the lack of use even among these young and sophisticated computer users. It's nice to be needed. Finally, I continue to see an opportunity for dramatic new organization and infrastructure in bioinformatics. The combination of incredible information overlap, in real data not just metadata, combined with powerful scientific and conservation implications for effective sharing means that there are huge untapped efficiencies. I continued to be inspired by the idea of a sub-internet, a "Bioinformatics Web" where conservation and scientific, especially conservation biology, data is entered, analyzed and leveraged in dramatically improved ways. Bottom line on this topic is that my work at NatureServe seems just the right thing.

As I said in my Conservation Economics post, I was moved by the irony of Costa Rica's acclaimed conservation programs and the realities of continued deforestation. Amphibian declines and ongoing hunting issues clarified the possibility of "empty forests". Secondary forests may indeed be the forests of the future, but if biodiversity declines continue, they will be characteristically quite different.

But it was the economic realities of conservation that I was most impressed by, specifically the need to develop the economic rewards of conservation and reforestation or be prepared for continued degradation. For instance, I was compelled by our discussion with Dan Jansen's and his bias against species-based conservation at the cost of simple acquisition and effective protection of intact landscapes or those suitable to reforestation that can connect intact landscapes. His views were characteristically harsh, but pragmatic. Dan also spoke with us about the accessibility that DNA bar coding may bring to non-scientists. I happen to agree that taxonomy need not be protected by the high-priests of today's taxonomists and that they is enormous education, and conservation, potential in making species identification increasingly cheap and easy.

Here again the theme of integrating local people into the conservation/restoration theme was clarified. Dan's work under INBio to train and employ local experts in taxonomy is a powerful alternative to the traditional, first-world-academia approach used by many conservation organizations. We saw another example the power of local knowledge in Cuerici where Swiss foresters controlled "sustainable forestry" practices. Secondary tree mortality resulting from the selective logging was much higher than the experts anticipated but completely consistent with the predictions of local farmers who know the forest.

In getting to know my fellow students, I was impressed and heartened by their talents and passion for their areas of expertise. I look forward to watching many of them progress to successful careers in science. I was surprised, I must say, by how some of the brightest minds among them seemed relatively unconcerned by issues in conservation. If nothing else, I would think self-interest in the preservation of their own systems would motivate some concerns. The course coordinators' inclusion of conservation and social science issues was thus all the more valuable to me.

I was also struck by the need for environmental education to encourage pragmatism and a system's approach. Even some faculty members took what I considered to be idealistic and unrealistic positions on the case for conservation that simply ignored historical, sociological and economic forces that must be respectfully confronted. In others I witnessed extreme pessimism about those same forces and a sense of helplessness. Both classes of response were recognizable to me from my own history. My experience in Costa Rica has clarified for me at a deeper level the need to stay positive, constructive and holistic in my own thinking and communication. Neither narrow idealism nor pessimism can be afforded.

There were some side lessons on leadership. My course coordinators struggled a bit to maintain good science content and keep logistics in order. Without going into too much detail, I can say that the course provided a small microcosm for the study of leadership and group dynamics. I didn't envy the coordinators' leadership challenges especially logistics in a foreign country and a bunch of opinionated students with sometimes conflicting needs. The experience gave me countless examples of the idea that leadership is best thought of as service ... and hard work. I particularly emphathized with the lonliness that leadership can sometimes bring, specifically the need to let go of being understood and even liked.

In these blog entries, I can see an evolution in my understanding of Costa Rica, natural systems and tropical biology research. What I will remember about Costa Rica is the combination of its natural beauty and conservation realities. What a fantastic and fun (!) experience.

0 Comments:

Wednesday, July 26, 2006

Swimming at Cabo Blanco

As a fitting end to our two month course, we went to the beach. Cabo Blanco is a secluded reserve on the southwest corner of the Nicoya penninsula where the forest meets the ocean. We spent four days at this beautiful site here doing our final field work. The snorkeling was fantastic and gave us a great opportunity to do underwater research projects.

My team worked with James ("Jimmy") Liao from Harvard's Department of Organismic and Evolutionary Biology. Jimmy has done some amazing work (cover of Science Magazine!) showing how fish optimize their swimming motion by slalmoning through areas of turbulance in streams. They change the cadence of their swimming strokes to 'bounce off' regular eddies or vortices caused by obstacles or other fish. In doing so, they use much less energy versus a normal swiming stroke.

Jimmy worked with our team looked to explore another (simpler) aspect of swimming biomechanics: fish morphology and potential correlation with habitat types. Paul Webb in 1984 proposed a "functional-morphology plane" that describes fish as cruisers (think tuna), maneuverers (think angel fish) or accelerators (think grouper) or some combination of the three.

We categorized the fish just off shore from Cabo Blanco as one of the basic three types and tested for coorelation to two different habitats: one closer open ocean and the other more protected and spatially complex. We did find a correlation between cruiser morphology with the habitat closer to open ocean and also between manueverer morphology and the more protected and complex environment. The project gave us some interesting exposure to concepts in evolution and specialization in the context of marine environments.

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Sunday, July 23, 2006

Conservation Economics

Monteverde's cloud forest is truly sublime with its distinctive dripping moss. The area has become one of Costa Rica's most famous destinations for ecotourism. In ironic support of that purpose, it's extremely hard to get to: the dirt road is long and jaw-crushingly filled with pot-holes. By this "neglect", the town of St. Elena and the Monteverde Reserve are discouraging day trippers from San Jose. You have to want it; you must commit. And if you do you'll spend more money and speak more favorably of it to your (wealthy) friends.

Founded by Quakers from the US in 1951, early ideas about ecotourism and its ability to make the economics case for conservation were developed here. Unlike most of Costa Rica's protected areas, the Monteverde Reserve itself is privately owned. In order to protect both the forest and visitors' experience of it, the Reserve limits visitors to 120 at a time into this 10,500 hectare property. The price of admission is $12, steep compared to most protected areas, but my sense is that travelers, especially Americans and Europeans, would pay more.

But should Costa Rica convert its economy to ecotourism? It's not an easy argument. Much of Costa Rica may not be interesting to tourists. Small rural communities, pastures, farms: these are not the places tourists flock to. Moreover, compared to agriculture or ranching, tourism is ephemeral. An international economic crisis renders a tourist economy vulnerable whereas the need for cows, banana, pineapple, rice and sugar cane remain.

Over the course of this trip, the irony of Costa Rica has become clear to me. Hailed as a model country for ecotourism, deforestation continues. Celebrated for its visionary park system, most of the parks are inadequately staffed and aren't valued by their surrounding communities. Traveling this landscape, dominated not by forest but by pasture and farms , it's hard not to see that assigning existence value to primary forest is a luxury of the wealthy. Since most of Costa Rica is accessible, even if by crappy roads, every parcel of forest that does remain must justify itself economically to those that own it, manage it and live on or around it. We're closer to the situation in which every tree persists because someone decided it makes some economic sense for it to do so versus a belief in its value as habitat (for monkeys, ants or birds) or its inherent tree-ness.

We spoke with some folks with Fundacorps, a sustainable forestry initiative sponsored in part by World Wildlife Fund, while at La Selva. From those discussions, it became clear that Costa Rica's carbon credit system isn't financially competitive with most other land uses. Furthermore, it's possible to log a forest and then invoke the carbon credit system for several years, then, when you're ready to harvest more trees, turn it off again. That may work well for sequestering carbon, but it doesn't incent the preservation of primary forest and all the biodiversity therein.

At as for the value of biodiversity itself, Merck Pharmaceuticals invested heavily in the protection of biodiversity in Costa Rica to enable "bioprospecting": the mining the forest for tomorrow's chemical compounds. As a consequence, INBio, Costa Rica's national biodiversity institute, was funded to inventory the nation's biodiversity. But Merck's investment didn't pay off. Productivity from synthetics research in the lab outstripped that of the primary forest. Merck has withdrawn most of its funding and INBio now struggles to stay viable.

For those who do see value in the forest's existence, the task is clear: find real economic value that actually pays the bills. That may be ecotourism, carbon sequestration or more abstractly insurance against catastrophe (similar to a diversified financial portfolio, a diverse species portfolio increases nature's chances of recovering from or avoiding disaster). But the value must be real and turn into hard currency for those who have the fate of conserved lands in their hands: local communities, local governments.

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Friday, July 14, 2006

Palo Verde

In the northern province of Guanacaste, the Palo Verde Biological Station sits just above an extensive marsh. The Tempisque river runs through the marsh and low mountains border all sides. We were warned of intolerable heat and mosquitos in this tropical dry forest, but I found neither particularly bothersome (at the time our of our visit, much of the US including DC was suffering an intense heatwave: I think we were much more comfortable than our friends back home). I was delighted by this station, perhaps because of the familiar dryness to my home state of New Mexico, but moreso because of its remoteness and extensive natural vistas.

We were joined at Palo Verde by Xavier Basurto, a social scientist working on conservation from the University of Arizona. Xavier works on community-based management of natural resources, an approach that I find both practical and heartening. I was so inspired by his description of the theory and framework for successful community management of common pool resources that I commondeered another student, Michelle, to work with me on an independant project to apply the principals to water management issues in the Tempisque River Basin. While the scope of our project was too small to allow a thorough examination of the the issues, it was a valuable excercise and one that I hope to pursue in other venues, both because of the importance of fresh water as an increasingly scarce resource and because of the justice and practicality I sense in the community managment approach.

On a walk to the river one day, we came across a troupe of howler monkeys lazily eating fruit from the trees over our heads. Here's one sunning himself, letting mango digest.

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Sunday, July 09, 2006

Tropical Forests = Carbon Source?

In the CO2-cycling machine planet Earth, tropical forests are on our side. Scientists have been telling us that climate change, caused by fossil fuel emissions, is mitigated by CO2 uptake of plants in the process of photosynthesis. But plants also emit CO2 in the process of respiration. Researchers at UC Davis recently reported that respiration appears to be essential to the growth of plants, perhaps in order to convert nitrate into a usable form, nitrogen. So when we talk about tropical forests as a sink for CO2, we're really saying that they absorb more CO2 than they emit. But under what conditions might this balance change?

My teammates on our "Biomass of Lianas and Trees" projectat La Selva, the site of Debra Clark's research

Debra Clark spoke to us one night about her research on long term tree growth at our host site, the La Selva Biological Station. It was a fascinating and rather disturbing talk where she emphasized the preliminary and unconfirmed nature of her findings ("Hubris, man!" was her call to scientists and politicians alike). Results from the TREES project show slower growth in years with higher temperature and decreased rainfall and that in the same time periods forests may have been overall sources, not sinks, of CO2. With increased warming and drought forecasted for the tropics, the result is that forests may actually contribute to climate change in a positive feedback cycle. At risk of sounding like Debbie Downer, the feedback cycle could be further exacerbated by increased fire and tree mortality.

Again, Clark's findings are highly preliminary, but we can say that the role of tropical forests in offsetting anthropogenic emissions is unclear. Based on what we do understand, the conservative course of action is clear: get moving! Change our priorities and create the economic incentives sufficient to end deforestation and dramatically curtail fossil fuel emissions.

Wednesday, July 05, 2006

Roxanne

To put it midly, these are interesting times for frogs, toads, salamanders and caecilians. On a global scale, amphibians are in decline. My own organization, NatureServe, was involved in an international effort to assess the state of amphibians and the news was not good. Nearly one-third (32%) of the world’s amphibian species are threatened, representing 1,896 species. By comparison, just 12% of all bird species and 23% of all mammal species are threatened. As many as 165 amphibian species may already be extinct. In Central America and other regions, frog species in particular are being devastated by the chytrid fungus. At the same time, La Selva as a site plays hosts to impressive amphibian diversity and as a biological station has a long history of amphibian research. So it seemed appropriate to direct one of my independent research projects while at La Selva to some investigation into frogs, these gems of species, this "charismatic microfauna."

I interested another student, Anna from the University of Indiana, in the idea of studying Dendrobates Pumilio, one of the poison dart frogs. D. Pumilio is a wonderous species: besides the beautiful red and blue coloring, they exibhibit interesting reproductive behavior. Males establish territories and call females to them with a distinctive “eh eh eh eh eh eh” sound. Males actively defend their territory against males of the same species first by issuing an “encounter” call distinctive from the mating call and, if the intruder isn’t deterred, engage in physical combat. The resident male usually wins the battle and the territory is his. After mating with a male, the females lay eggs in the forest leaf litter. Males have been shown to guard the eggs until they hatch, afterwhich one of the parents will carry each tadpole on its back to a separate bromeliad plant high in the tree canopy. At this point, female returns daily to lay unfertilized eggs as food for the growing tadpole.

Anna and I decided to conduct an experimental study on the communication mechanisms of D. Pumilio, auditory, visual and behavioral. Our species was easy to find at La Selva as males continuously announce their presence in form of mating calls and of course distinctive coloration makes both males and females relatively easy to spot. As part of the territory defense, we hypothesized that males would respond first to the sound of a competitive male intruder, then to its image and finally to signs of aggressive behavior. Seems pretty intuitive, sure, but this is OTS and we only have a few days to design, execute analyze and present our study. To test our bold idea, we needed to separate these communication mechanisms and compare them individually and in various combinations. Our plan was to choose an actively calling male and present him with one of these combinations of simulated sound, image and interactive behavior and measure his responses.

For sound, we started with recordings of the mating call of a few sample males and an encounter call we downloaded from the web, combining them into a single hour long recording. Ours would be a frog with endurance. Lacking a better playback device, we took a course laptop in a plastic bag with us into the field (shhhh!). For image, fortune smiled upon us: another study was going on at La Selva into bird predation on our same species and that team gave us some clay models that gave a pretty good visual impression of a single individual. And finally for behavior, we used a small mirror, the idea being if the sound and image pulled a resident frog in, we could observe the frog interacting with its own dynamic image. We conducted a total of 14 different tests of around 15 min each with various combinations of image, sound and the mirror and measured responses from the resident male.

The first thing we learned is that frog habitat makes for excellent mosquito habitat: we donated a lot of blood while trying to stand still for 15 minutes at a time. That aside, our much basic hypothesis seemed to be valid. The most successful configuration in terms of generating responses was that of sound combined with image followed by sound alone. In one particularly exciting instance involving both sound and image, the resident male approached the model and circled within a few centimeters many times, returned the (more aggressive) encounter call, and seemed “puff” itself up by standing taller on its front legs when approaching our clay model. Our sample size was too small and results to varied for our study to be taken seriously, but it helped us develop an interesting protocol on which a more complete study could be based.

Finally, we found a cool program on the web that proported to provide semantic translate D. Pumilio calls. We ran some our recordings through the program and found an interesting section in which the translation came out as this: “eh eh eh eh, eh eh eh eh ... Rooooxane. You don’t have to put on the red light….” That joke might not work well here on my blog, but it killed in our final presentation to the course.

Here's a female crawling around on Anna's shirt. Don't worry, their poison is only toxic to small preditors. This was a delightful project because our subject was so engaging. It was all made bittersweet by the knowledge that this species, like so many frogs, may not be long for this world.

2 Comments:

The fact that us Africian Clawed Frogs are immune to that fungus just shows that we are superior to other frogs. Their females should just accept us as mates instead of being like that human female EPA scientist & lesbian in that movie Frog-g-g!http://www.froggg.com/

For paranoid types (a loose term in these Bush Administration years), Lab_Frog, being a unique species because of genetic experiments on the International Space Station and currently living at his secret lunar base, has no intention of attempting to mate with human females. Too unlikely to be genetically combatable and too far.

Thursday, June 29, 2006

Death of an Oak

Tree falls have significant impact on forest dynamics: returning nutrients to the soil, completely changing the light availability to the forest floor around them and wrecking havoc on the neighborhood of other trees and lower reaching plants. In the lower tropics, it takes an average of 137 years for the forest to refill the canopy gap left after the fall of a mature canopy tree. Here in the highlands of the Tamanaca, it’s likely to be much longer as these oaks may only grow ½ a meter in a decade.

Though you may be mighty, there are a number of ways to loose your life as a large canopy tree. On the other end of the spatial scale, you chief risk is micro and macro-organisms that will literally eat you from the inside out and outside in. Fires are extremely rare here but several have started in the last 100 years from neighboring farms and residents allow them to burn. The resulting fire damage can open a wound at your base allowing for disease and decomposition of your bark. Placement of your roots is critical, especially if your life began, ever so long ago, as a seed on a steep slope. In this circumstance, you will cling to the forest floor by the high anchor point of your root system and if something should compromise it, such as the root system of a neighboring tree, death is certain. The death of a neighbor also poses huge risk for when it falls, if it doesn’t take you out instantly, it can take off on of your branches, creating an opening for those that would feed themselves and all their progeny on your insides, all the way to your roots, eventually unearthing you too.

Most trees decompose through their core, usually because their core has been compromised. In this case, all that they were becomes food for the forest itself. If, however, a tree falls with its core in tact, especially in less moist microclimates, it will loose bark and cambium but retain that core for a very long time. We saw some trees in the forests of Cuerici that were almost shiny with wear and hard as rocks, fossilized where they fell.

I’ve teamed up with Laura Vary, a fantastic botanist, to look at tree falls and succession here in the cloud forest at Cueraci. The section we’re focusing on is dominated by a native bamboo, Chusquea, and two native species of oak, Quercus copeyensis & Q. costaricensis. Our aim is to describe a community succession pattern on a single species of oak based on age of the tree fall, light availability and health of the tree when it fell. Central to our study is the knowledge of our host here at Cueraci, Carlos Serano, whom we all call “Don Carlos”. Pictured below, he has helped us to find, age and diagnose a set of fallen oaks. From there, we catalog the set of plant (and possibly fungus) species present and look for patterns. Having no idea if any of this will amount to anything interesting, our day was nonetheless fascinating. Don Carlos shared his deep love and knowledge of the forest with us and showed us a monster tree fall: the death within the last 30 days of a thousand-year old giant. The fall of this single tree, pictured at the top of this post, took at least four others with it and left an enormous and precious light gap in the midst of otherwise tight canopy.

The next day we had an even more immediate experience of this phenomenon. Standing on the fallen now horizontal trunk of this enormous tree, we were stunned by a sudden cacophony of cracks, pops, followed by crashes and thunder from the ground. Over my left shoulder I glimpsed a large tree just beyond the clearing fall away to its death. I looked back at Laura as we both erupted with amazement. We waited 10 minutes and approached the scene tentatively in case the full domino effect of this newest tree fall had not yet played out. We arrived to find fresh dirt covering everything in proximity to the tree’s root system. Here’s a picture of the freshly fallen and the remnants of an unlucky neighbor.

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Tuesday, June 27, 2006

Cuerici

We left Las Cruces in style, a rather cushy bus. Bus rides are the place for these youngsters to recover from the "final night at a station party" so sleep and iPod rule the day. The Interamerican Highway is impossibly narrow for two cars going in opposite directions, not to mention a semi and a bus... ours. I choose to look away and trust, but I shutter to think of Holli and I renting a car after the course and braving these roads, knowing what I know now.

Departing the bus, we switched to jeeps and finally arrived at our destination high in the Talamanca mountains. “Don Carlos” is the owner and manager of this 350 ha parcel and small station in the sky, our home for 7 days. Carlos’s family managed the property for forestry but his innate curiousity in nature and exposure to travelers with a conservation focus eventually instilled in him an impressive balance of necessary use and protection where and when ever possible.

Our surroundings are dramatically different from the relatively lush accommodations of Las Cruces. We sleep in a large bunk room in tight quarters and the lab/work building next door has absolutely no connectivity (thus the lapse in my postings). The socially intense environment is completely offset by our isolated surroundings. Primary cloud forest is just out the front door and the reliable afternoon rains pounding on the tin roof are surprisingly soothing, a delightful reminder of my childhood summer afternoons in my family’s rustic cabin in the Ruidoso, New Mexico.Don Carlos makes excellent use of the intact core of fallen trees, so all buildings at the site are made of beautiful wood. Nights are quite cold so we gather around a huge fire place (wasn’t this supposed to be the tropics?) for evening lectures on the basics of vascular plants, plant breeding systems (challenge: mature and have sex all while being stuck in the ground your whole life), the fascinating social systems of leaf cutter ants or a rather dry stats review. Much of what I learn, I learn from my fellow students. I’m inspired and humbled to join them on this course and together experience Costa Rica’s diversity. This picture was taken on one of our first walks at Cuerici as the late morning mist rolled in.

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Monday, June 19, 2006

Ecology in the Field: Bromelania!

The second day here at Las Cruzes, Peter tasked us each individual to a 20 minute walk around the immediate area to conjure up a set of ecological questions at various scales: individual, population, community, and landscape. Beyond that structure, whatever came to mind was allowable in this game of organized wondering. Within moments of my solo walk, I came upon this lizard (not my picture), ameiva festiva, Costa Rica’s only whipped tailed lizard, I later learned.I remember coming upon whipped tail lizards in New Mexico as a kid, many missing their tails. So I ended up spending my full 20 minutes with this one lizard and instead of thinking about how I could catch it, like I did when I was a kid, I started asking questions about its diet preferences, how much it had to eat to maintain such high metabolism, etc. I wondered how the lack of a top predator in the ecosystem (jaguar) has effected is abundance, does its range include some of the habitats undergoing restoration and how might it contribute to that restoration. I won’t bore you with all of the questions, but the one I settled on to bring back to the group was a curiosity about the way the lizard’s metabolism, ability to hunt and mate was affected when its tail was sacrificed. The lack of tail might compromise its movements in significant ways and at the same time growing back that tail takes energy itself. Limited resources would be allocated differently but would the lizard be more or less conservative in its hunting and might it forgo mating-related activities altogether? Many of these questions if not all are surely answered in the scientific literature, but I found the exercise both enlightening and quite a lot of fun.

The walking exercise is now being put into practice at a different scale: we’ve broken up into teams and pursuing a single research question. My team in particular is trying to establish whether the microbial community in a bromeliad is facilitated by the plant itself in some way. Does that sound fascinating? Well, like all things, you get close enough to it and it absolutely is. Totally fascinating. I’m on the sub-team that’s ironing out the experimental design. Our aim is to both describe the micro community in terms of richness and abundance of species and then conduct an experiment where we compare a bromeliad plant (neoregelia carolinae) to a “cup of water” to see if there’s something about the plant itself that facilitates community development. All in 3 days of work.

So far, our plan is going well. We’ve identified a total of 30 individual plants to work with (conveniently located here in the Wilson Botanical Garden) and described the community composition in a set of 10. For the experimental component (a manipulation of nature to make a point!), we extracted the contents from center column of the other 20. In ten of those we filtered the contents through tight mesh to remove the micro-community and returned the remaining water, with its “natural” chemistry, to the plant. In the final ten plants, we removed the contents and replaced it with rain water. Here’s one of my teammates extracting the water-based community from one of our experimental bromeliads.

We next set up a set of controls: plastic cups interspersed in the field of bromeliads. We cut holes all to give them a comparable volume to that of our average bromeliad and then broke them into groups containing either rain water, rain water with a “swish” of the filtered bromeliad water (to control for limitations in extracting all of the community from the bromeliad plants), or filtered bromeliad water as in the plant treatment above. Then we let the whole experiment “cook” for several days.

Yesterday was spent at the microscope. I haven’t looked through a microscope in any kind of serious way since high school! But there we all were with micro community taxonomy texts on hand separating and counting ostracods, mites, branchipods, midges, nematodes, copepods, mosquito larvae, and sorts of tiny spiders, ants, bees, flies and even a cricket. Moving from the microscope to the computer we are in the midst of analysis to compare the biodiversity (measured in our case as “evenness”: the number of difference species and abundance of each species) in each of the treatments. If our hypothesis holds out, we should see more diversity in the plants versus the cups and more diversity in the “naturalized” water over the plain rain water in both plants and cups. Here’s one view of our draft results, a “rank-abundance” which gives a graphical view of both richness (number of different species) and abundance (number of each species). Turns out there was too much variance between the results from each treatment type for our study to be considered valid, but we did see a pattern in the direction of evenness for the cup treatments and species dominance in the bromeliads. My teammates have brought extensive expertise to bear on the project. It’s going to be interesting when I have to do an ecological study all on my own in a few weeks.

3 Comments:

I am really interested in the whipped tailed species. Is it true that this particular species is all female and all they need is stimulation to reproduce rather than actual penetration? I read this on Yahoo and have been researching and cant find any information.

Wednesday, June 14, 2006

The Art of Ecological Research and Strangulation

Yesterday we walked through secondary forest with an assignment to identify interesting questions we could imagine researching in just a few days. Lots of fascinating forest ecology stories were told including the delicate mechanics of orchid pollen exchange, but the focus was on the development of research questions. Having no background in research, this was for me a wee bit of a challenge, but this first step in question development seems to be about pursuing any given wonderment with a mixture of rigor and imagination. What I have less of is the knowledge to inform my wondering… having a sense for the fundamental dynamics that, in a given context such as this secondary forest, will give rise to questions about how those dynamics might manifest or how certain phenomenon might be explained.

So for instance, what forces drive variation in activity level in the monkeys of Costa Rica? Now a bit of context: Howler monkeys are relatively sedate, spider and the white faced monkeys have intermediate mobility, and squirrel monkeys are highly mobile. And now some theory: resource availability, competition, maybe even reproduction (we’re back to sex again!) all might play a role. So what specific questions might I ask to understand the variation? I might hypothesize that it has something to do with resource availability (variation in diet) and, perhaps further, specialization of diet from competition. Now I can survey the populations and observe eating habits directly or indirectly (say through their poop! Or should I say “scat”). I might also create an experiment to directly test my hypothesis, changing the normal patterns I observe in some decisive way that lends itself to illuminating measurement. I see the logic and beauty in this approach, so fundamental to knowledge but so new to me in such an elementary form. From there, the software developer in me is comfortable, if only conceptually, with the engineering problems of experiment design and execution: think of ways to answer the questions, define a design, look for and address potential defects, all the while being ready to change strategies when necessary. I can see that there's an art to experiment design, one that takes talent and dedication to develop.

And now to the art of a strangulation. Along the walk we came across a huge strangler fig (family moraceae, genus ficus) a plant with an amazing strategy for establishment. The parent strangler fig produces fig fruits that get eaten by, oh, say, by a spider monkey. The seeds, if all goes well, find a happy environment in the niche of a tree in the canopy and germinate, dropping roots from the canopy the forest floor, possibly far below. Where before nutrients were extracted from the host tree and growth was slow, the fig now sustains itself on ground nutrients and grows quickly in a lattice around the trunk of the host tree, upwards towards the canopy. The host and the fig now compete for precious light and ground nutrients, but the fig also “strangles” the host, constraining its nutrient flow and growth. Eventually, the host dies and rots inside the lattice structure, providing further nutrients for the victorious fig. I imagine there might be cases where the fig is overly ambitious, killing its host tree before it’s fully established and able to maintain structure, so there is perhaps an art to the timing of the kill. On our walk yesterday morning, we came across an example of a successful strangulation: a hollow tunnel to the sky where the host once lived.